The '59 in the neck - no, it's just RW/RP to help cancel noise when the PU selector is in the middle position. The PG "plus" - yes, those were made special for Fender guitars, AFAIK.
nah, i think you have it right. the 59 is only custom due to the polarity switch but the pg+ is basically just a pg with an alnico 5 magnet rather than the standard alnico 2
That's easy. The neck part goes without saying.
As for the bridge, if the only difference is the magnet then it's really easy to just get an AlNiCo 5 bar and replace it with the AlNiCo 2 the standard Pearly Gates has